Fig. 4.

Mapping of non-MTB reads across the MTB reference genome impacts variant calling. a Mean sequencing depth along the MTB reference genome across 1000 bp windows when mapping 1500,000 simulated reads of non-tuberculous mycobacteria species and organisms other than mycobacteria (OTM). For OTM, the 10 organisms that produced higher sequencing depths are shown. b Number of false positive vSNPs and false negative fSNPs (note log scale) in samples in silico contaminated with different proportions of non-MTB organisms when following 3 different analysis pipelines (taxonomic filtering, similarity filtering, and a standard pipeline including a mapping quality filter (MAPQ 60))